Southern sympathizers in Baltimore cut telegraph lines and bridges to Washington, D. C. While passing through the city, the 6th Massachusetts Regiment is attacked. They open fire on a crowd. When the dust settles, three soldiers and one civilian were dead, the first casualties during fighting in the Civil War.

From the outset, Southerners questioned whether Maryland would join the Confederacy, as did most of Washington, D. C.. Governor Thomas Holliday Hicks sent a number of pro-Union signals in speeches dating back to 1858 ("Maryland is devoted to the Union"). By 1860 the governor was saying "...if the Union must be dissolved let it be done calmly, deliberately, and after full reflection..." In a letter dated November 27, 1861 Know Nothing (American Party) Governor Hicks explicitly refused to call a secessionist convention in Maryland stating "I see nothing in the bare election of Abraham Lincoln that would justify the South in taking any steps tending toward a separation of these States."

On December 6 the Democrat legislature agreed, passing legislation that said, in part, "we will firmly resist being dragged into secession." Governor Hicks reiterated his intention of not calling a secessionist convention on January 5, 1861 (This address was published on January 6, which is sometimes given as the date). For two days (February 18-19, 1861) following the formation of the Confederacy, the legislature decided to call a convention. Representatives from each county met in Baltimore to discuss secession, but the "Conference Convention" fell short of planning any action. Instead, they simply recommended that if Virginia seceded, then Maryland should also secede.

When the first shots were fired at Fort Sumter only seven states were in the Confederacy. Sumter, however, solidified support for the Confederacy and Virginia, Tennessee, North Carolina and Arkansas quickly followed the other slave states. The remaining states with a large number of slaves (Maryland, Kentucky, Missouri) were more deeply divided because large portions of the electorate did not support slavery.

While the Lincoln Administration began working quickly to keep the remaining southern states in the Union, they had a serious problem with Maryland because of its location. Situated between the North and Washington, losing Maryland to the South would make it difficult for the Lincoln Administration to remain in the city, especially during the early phase of The Civil War. Pro-South protesters led the Baltimore Riot of 1861 on April 19, attempting to halt or delay troop movement to Washington.

When the riots were over, Governor Hicks, Baltimore mayor George Brown, Ex-governor Enoch Louis Lowe, and Marshall of Police of Baltimore George P. Kane met to discuss the situation in Baltimore. To eliminate the chance of additional troops passing through the city these men decided to destroy the railroad bridges around Baltimore, which occurred on the night of April 19-20, 1861. According to the other men, Hicks gave the order to destroy the bridges, which Hicks later denied.

Governor Hicks returned to the state capitol in Annapolis. On April 22, 1861, Benjamin Butler showed up with a boatload of Union volunteers making their way to Washington. When Butler arrived in Philadelphia on April 20, he had been unable to advance because of the burned bridges, so he commandeered a boat to get around Baltimore. In the east, only the area near Baltimore was considered pro-slavery. To the west, many of the counties had voted for John Breckinridge, the dashing pro-slavery candidate for President. With Annapolis under Union control and Baltimore subject to mob rule, Governor Hicks ordered a secessionist convention to form in Frederick, in the western part of the state starting on April 26, 1861.

On April 27 the body announced that it did not have the power to "commit this state to secession." In the end, the convention would vote 53-12 to call a secessionist convention if the people of Virginia seceded. The convention, however, did not adjourn and continued to meet throughout the summer. On May 2, 1861 Rebel sympathizers in Baltimore were cut off from communication with the South by a large federal force at Relay House, south of Baltimore on the B&O. George Kane was arrested for having a role in a plot against Lincoln as he moved through Baltimore in February, 1861.

Secretary of War Simon Cameron asked George McClellan to arrest all pro-South members of the secession convention called for September 17. That day, orders were issued by McClellan for Nathaniel Banks to make the arrests and Major General John Adams Dix, commander of the Department of Maryland and the Department of Pennsylvania was given the duty. Among the first men arrested was Baltimore mayor George Brown, on September 12.

Over the nine days Dix made arrests, however, when the convention convened on September 17 (six days later), a quorum could not be established and the Maryland secession convention came to an end. On September 20, 1861 Dix arrested E. G. Kilbourn, Speaker of the Maryland House of Delegates. Kilbourn was characterized by Dix as being a "dangerous secessionist." Kilbourn remained in federal custody at Fort Warren (in Boston Harbor) until February 15, 1862.